Talk:MiPNet19.03 O2k-cleaning and ISS
- 1 Popular Bioblast page
- 2 Contamination with hydrophobic inhibitors: The experiences with TPP electrodes
- 3 Apparent carry-over of CI-inhibitors versus contamination in chemicals (update: solved)
- 4 Cleaning with diluted acids
- 5 Protein Contamination
- 6 MiPNet discussion forum: cleaning the glass chamber (2017-02-28)
- 7 Isopropanol vs Ethanol
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Contamination with hydrophobic inhibitors: The experiences with TPP electrodes
- We had problems with inhibitors carry over during the experiments with TPP electrodes. Despite of all the standard cleaning procedure of the chamber and electrodes, the inhibitors were present in next experiment.
- We rinse the electrodes after use with water, dry with paper, rinse with absolute ethanol, again dry with paper and rinse with water again. This procedure is sometimes not sufficient.
So we decided to put the electrodes rinsed with this procedure into a falcon tube filled with water for a while (15-30 min). After the standard washing of the chamber with water, 70% ethanol, absolute ethanol and water we did washing of the chamber and electrodes (in the chamber) with liver homogenate. It really helped to get rid of all the inhibitors in 90% of cases.
We are very careful with using syringes and cleaning them after each titration if the inhibitor was present already in the chamber (wash them with water by putting them in falcon tube with water drying with paper and putting to ethanol and drying with paper again). For each chemical we have a separate syringe. We wash it after the experiment and store filled with absolute ethanol and with the tip in absolute ethanol (in falcon tube). Also each TPP and reference electrode has its own falcon tube with storage solution.
Zuzana 11:08, 9 December 2010 (CET)
Apparent carry-over of CI-inhibitors versus contamination in chemicals (update: solved)
We have been trying your suggestion about using liver homogenates to check the problem of our Oxygraph-2k. I am happy to see that your suggestion works, but not completely, as you can see in files attached. You will find files from two different O2k instruments. In summary, first day after letting liver homogenates to incubate with PM we did not see any response when we have added ADP. We washed and let it stay for few hours with a new liver homogenate and the good news is that one of the chambers responded to ADP addition after PM (first time since I am here that I see this response in liver). So we decided to continue with the treatment with both Oxygraph and we got 3 of the 4 POS responding to ADP after PM in liver homogenates. Two days ago we have tried then to test hypothalamus to see if we are able to see the responses I use to see in these homogenates and you can take a look to the file “2012-02-15 Hyp-liv” we saw an small effect of ADP after PM but far from the one I use to see (the addition of Succinate as always works well). In general, I think we are in the right track but it needs a more strong washing of the carry-over effects of rotenone or other inhibitors (I started to think after analyzing many files that this problem is being present for a long time and that the concentrations of the inhibitors are above recommended even they were prepared several times) This high concentration of the inhibitors could explain that after incubating with cells for several hours still we come back to the same problems for continuing using the same titrations of the inhibitors. However I am not so sure about it and I will test the concentration once we solve the problem and we can be sure that we do not have more carry-over effects. Do you have any suggestion of how can I get read of the carry-over effect? Once we solve this we could check if we have solved finally all our problems and we can start to work in our projects using the PBI-Shredder.
How to continue
The problem of washing/carry-over of inhibitors is an extremely important issue. In our projects (practically always involving 4 to 6 O2k-Instruments with 8 to 12 chambers in parallel) we have had phases (largely unexplained) where such problems became apparent, and then (partially unexplained) they disappeared.
Consider that you would not have the experience of your experimental phase at Karolinska. Probably, either, you would not recognize the methodological problem and run into a series of unnoticed artefacts, or you would put into question the entire approach. We have not encountered the latter scenario - according to all the feedback received or not received from more than 350 labs . But I am afraid, that there is a grey zone of labs that use problematic results uncritically (without having the necessary experience). Hence the problems your are facing (and which hopefully will be resolved soon) should be communicated to the O2k-Network: Perhaps the corresponding feedback may help us to solving the problem more quickly. Or perhaps, at this stage it may merely be an educational pathway for sharing the experience with others. Therefore, we should aim at providing a summary of this – hopefully successful – trouble shooting, in the spirit of QA and Gentle Science. At OROBOROS INSTRUMENTS, I want to implement the strategy of OPEN INNOVATION. Open trouble shooting has to be part of it.
Now some considerations coming back to the specific problem. We are not alone with this problem. Some groups using conventional oxygraphs (with Perspex chambers, Teflon stirrers etc) have long avoided some carry-over effects by strictly separating chambers with application of rotenone from chambers without. This, however, is not satisfactory for us, since it precluded application of our complex SUIT protocols. But if the apparent carry-over problem is only partially resolved, it would make sense to try a series of very simple experiments, when one O2k-Chamber is reserved for CI-linked respiration, without further addition of a CI-inhibitor. Still you can add succinate after CI-linked substrates. A series of such runs would reveal higher CI-linked OXPHOS capacities compared to chambers where CI-inhibitors are regularly used. This would not represent a finally satisfactory state, but could provide a next step for diagnosis of the underlying problem. Perhaps we may find some new-generation strong glass-ware detergents or other stuff, which destroy all these inhibitors but can be washed out more easily (so far, I stayed away from detergents other than saponin and digitonin). Perhpas it might be even worthwhile to try digitonin as a washing reagent (???).
I a series of experiments with the TPP+ ion selective electrode, we encountered a washout problem that increased over several months. Originally some outliers were observed occasionally. And within several months, the problem become more dramatic, with more than half the chambers remaining suspect. At the same time, no carry-over effects were apparent in the same chambers, when no MultiSensor experiments were carried out. The phenomenon remained mysterious, and our PostDoc project was finished without resolving this crazy issue. Other groups using our TPP+ electrode did not run into such an extreme problem (so far?). Our current projects, and the TPP+ demos at our workshops, did not reveal this carry-over problem. But it may start again tomorrow!?!
I hope by combining the critical observations from various experimental settings, we may shed some light on these problems, hopefully developing a general solution.
Many thanks for your patience, open discussion, and good luck to all of us in finding a lasting solution.
--Gnaiger Erich 21:31, 17 February 2012 (CET)
Testing the chemicals
Today we have performed another experiment looking for the solution of our Oxygraph-respirometry problems. In order to be sure that what we are facing is a problem of carry-over of inhibitors due to an excess in the titrations or a defect during the washing period, we decided to perform another experiment. This time the idea was to test that all our substrates and media that are involved in the non existing response of Complex I substrates to ADP addition (M, P, G, ADP, MgCl2, and MiR05) were tested in a different Oxygraph-2k from another group, which does not experience any problems with inhibitors. If our experiment works well in their O2k, then we will be more certain that the problem is a carry-over effect of the inhibitors in our O2k-chambers. However, the results of this experiment tell us that this is not the case, because we got the same problems (lack of response to ADP in liver and hypothalamus homogenates in MiR05 with M+P+G) - same results as experienced in our O2ks. Then, if we exclude a carry-over effect of the inhibitors as the source of our problems (I am not 100% sure about it yet), what could be the reason for this lack of response to ADP?. Again, as always, addition of succinate after M+P+G+ADP increases respiration dramatically. - Pablo 2012-02-22
I agree, you are now zooming in on the quality control of the chemicals, in contrast to a potential carry-over of inhibitors from the O2k-chamber. You tested the medium MiR05 before, without indication that this is the source of inhibition. Then the added chemicals have to be tested. In an early phase of bioenergetics, ADP was noted to be contaminated by zink. Zn2+ is an inhibitor of CI-linked respiration and less potent for CII-linked resipration (Brown et al 2000 PMID: 10788456; Ye et al 2001 PMID: 11226237). The best test would be to repeat your experiment using all chemicals from the other lab in your O2k. If you would get now the expected ADP-stimulated OXPHOS capacity, then you could immediately titrate you own ADP, followed by your M, P and G. Perhaps you would observe an inhibition after one of these titrations. Then the problem would not be specifically related to the 'hydrophobic inhibitors'. Quality control of chemicals (applied in our media and SUIT protocols) is a very general emerging problem, which requires new strategies to be solved. - --Gnaiger Erich 11:34, 22 February 2012 (CET)
The problem was finally solved. Some of the ethanol used in Pablos lab contained small quantities of an antiseptic. See Biological contamination and MiPNet19.03_O2k-cleaning_and_ISS#Unintentional_introduction_of_inhibitors_to_the_O2k-Chamber
Cleaning with diluted acids
Question: Colleagues and I want to introduce heavy metals into the chambers of the oxygraph-2k. We were wondering what that would mean in terms of cleaning: Would acid-washing the chambers with either 0,1-0,3N HNO3 or HCl be a problem for the membranes?
Answer: The glass chambers and membranes (FEP) would not be a problem, but some polymeric components might. Therefore, we tested approx 0.3 M HNO3 over night at room temperature plus 2 hours at approx 35 °C on the following materials: FEP (POS membranes), PVDF ( white stoppers), POM O2k-Chamber Holder), butyl rubber ( OroboPOS-Seal Tip, and Viton O-ring\Viton\12x1 mm. No immediately visible problem was detected. Frequent or prolonged use might of course still have negative effects. Since HNO3 was nor problem for the polymers (non oxidizing), HCl of similar concentration is presumably save.
Of course 0.3 M HNO2 is still a rather mild way to deal with heavy metal contaminations. Classical methods (cocentrated acids) would require to remove the glass chamber and clean it outside the O2k as described for protein contamination MiPNet19.03_O2k-cleaning_and_ISS#General_cleaning_instructions. Fasching Mario 15:45, 20 August 2014 (CEST)
I have trouble cleaning the glass chambers of what I think is protein contamination as described in the cleaning protocol. The whitish layer in the lower area of the glass chamber appears to be unimpressed by my cleaning attempts in conc. HCl over the weekend. I am now thinking about using Chromic acid to clean it. Does this make sense, what else can I try? Any comments on that, please. Thank you and greetings from Ireland
Answer: when removed from the oxygraph, the glass chamber can be cleaned with all agents used for laboratory glassware (Duran), including chromic acid. However, sometimes it is difficult to differentiate between scratches in the glass and contamination on the glass. Therefore, after the HCl conc. treatment I would first reassembly the chamber and observe whether there are any remaining problems observable:
- is the stirrer jumping?
- is the uncorrected oxygen flux at closed chamber in water higher that it should be? See Flux at closed chamber near to air saturation.
If yes, the cleaning procedure has to be continued, but if no I would guess that the remaining contamination is rather scratched glass unless it is very obvious that there is some foreign material on the glass wall. Slightly scratched glass is usually not a problem.
Mario 14:49, 10 January 2011 (CET)
Feedback: The stirrers kept jumping and I still got unsteady readings, so I cleaned the glass chambers with chromic acid stirring over night, reassembeled everything and perfomred a sensor test. I conlcude: if nothing else helps, chromic acid is your weapon of choice. Thanks for your help Mario.
Manni 12:48, 9 February 2011 (GMT)
MiPNet discussion forum: cleaning the glass chamber (2017-02-28)
After working for some time with tissue homogenate, I noticed quite a bit of turbidity on the chamber glass. I tried cleaning it with HCl, Chromic acid and proteolytic enzymes (all overnight), but could not get rid most of it. I also tried the ultrasonic treatment, again without success. Do anyone have any other suggestions and experience with this issue?
I had a similar problem but using particularly intensively isolated mitochondria and permeabilized cells. HCl treatment was not successful, but I could get rid of the material by simply cleaning it with a cheesecloth gauze. I don’t know if this will work in your case but you can give it a try. Best Regards, Marco Spinazzi
Try 50% household bleach and water, it strips the protein off in the chamber while the stir bar spins. But wash and wash the chamber afterwards. You will see the stuff lift off the glass. The membrane is fine. Tony
Have you tried 5 minutes in soft drink bath? https://m.facebook.com/story.php?story_fbid=10206394904191511&id=1835332703
Ib Therkelsen Arent
Try Cotton buds (ear buds) to mechanically wipe off the dirt. Cheapest sort will do. This is our ultimate weapon around here. It's like your favorite tea cup; at times you need to clean its inside properly with a scrub. Just pouring random chemicals into it won't work. - I'm surprised, though, that Chromic acid didn't do the trick. It's famous for destroying almost everything... Best regards, Ib Therkelsen Arent
Isopropanol vs Ethanol
Question: I like the idea of using isopropanol because it is cheaper and does not required the paper work that pure ethanol do (for us in the States)! Isopropanol is the common alcohol used in clinic and hospital to clean skin so it is safe too.
I found a chemical compatibility search engine at  and I would like to know if the following materials are part of chambers? Acrylonitrile butadiene styrene (ABS), CPVC, Hytrel®, Kel-F®, Nylon, PPS (Ryton®), and PVDF (Kynar®).
If none of these would be in contact with the cleaning solution, I believe we should be able to switch to isopropanol to get rid of biological contaminants.
Dear Fran, PVDF is on your exclusion list because no data is available for PVDF/isopropanol on the site you mentioned. However, PVDF /isopropanol should be fine according to our data. In fact, I once did a quick search for material compatibility with isopropanol and some other substances for all affected parts of the oxygraph. This was to find a "denaturated" ethanol that would be compatible with our system. The result was that isopropanol would be just about the only acceptable denaturation agent. Unfortunately its not defined as a denaturing agent by Austrian tax law, but I would dare to use it as a denaturing agent in a country where it is used for this purpose (like Germany). However there is big difference between using only a small percentage as denaturing agent in ethanol or using pure isopropanol. This effects both potential problems:
a.) Material compatibility:
Before using 100% isopropanol I would repeat (and in more detail) a internet search for the affected parts. I would try to find at least two internet sources for each combination. The affect parts are:
- all kind of O-ring\Viton\12x1_mm
- and either Stopper\black_PEEK\conical_Shaft\central_Port or Stopper\white_PVDF\conical_Shaft\central_Port
The material is described on each page. I took this opportunity to add this information where missing. Your stoppers may be either white (PVDF) or black (PEEK). The POS is PEEK, the stirrers PVDF, so you have to include both PEEK and PVDF anyway.
b.) Sterilization power: Please note that the mixture 70% ethanol 30% water is a particular strong sterilizing agent (stronger than e.g. pure ethanol). As far as I know (and I am certainly not an expert) isoproanol is also used in hospitals because it is comparable nice to human skin. Therefore I would look for literature concerning a comparison 70% ethanol with any isopropanol mixture before attempting the switch. Such literature could also hint at a suitable water isopropanol mixing ratio. Fasching Mario 09:42, 22 January 2013 (CET)